Thursday, April 25, 2013

The compiling of the components below are quite expected.
boost,
eigen,
samtools

But when finally compiling cufflinks, you might encounter errors

.....
.....
checking for bamlib... configure: error: We could not detect the bam libraries
(version or higher). If you have a staged bam library (still not installed)
please specify $BAM_ROOT in your environment and do not give a PATH to --with-bam option.
If you are sure you have bam installed, then check your version number looking in.........
See http://randspringer.de/bam for more documentation.

The source of the error is somehow the cufflinks is not able to find the libraires and binaries found by samtools. This is especially true if you compiled the components into distinct directories and not into standard directories like /usr/local/bin and /usr/local/lib /usr/local/include

To ensure that the cufflinks detects the samtools libraries, you might want to do the following.

Monday, April 22, 2013

I installed a non-commercial version of Intel XE 2013 and realise that I wanted to change the installation directory. I realise that for Intel XE 2013 does not have an uninstall script (install-dir/bin/uninstall.sh) like previous version.

A simple removal of the intel directory does not allow me to have a good clean installation like choosing installation directory.It is likely due to the presence of rpm information still remaining in the rpm database.

To solve the issue, I use the command

# for i in `rpm -qa | grep intel` ; do rpm -e $i ; done

You may need to run the command 2-3 times to ensure all the dependencies and intel packages are totally cleaned up

Friday, April 5, 2013

Chelsio
Announced the Terminator 5 ASIC, a highly integrated, hyper-virtualized 10/40GbE
controller built around a programmable protocol-processing engine, with full
offload of a complete Unified Wire solution.

Wednesday, April 3, 2013

For a cluster shared by many users, it is important to prevent errant
users from directly ssh into the compute nodes, thus bypassing the
scheduler. To implement the pam module, compile the Torque Server based
on Installing Torque 2.5 on CentOS 6
Step 1: You should be able to find the pam_pbssimpleauth.so packages at